1) Do you have a backup of the files that live in that datastore? If so, you can simply power down tthe VM, right-click and "Remove From Inventory", copy the backups into the appropriate location, then find the VMX file on the datastore, right-click and "Import" and it will bring the VM back to life in the state it was in during the backups.
2) Have you searched the parent folders for if this file was mistakenly moved?
3) Do you guys have Automated DRS enabled (vmware can vMotion a machine if it deems it necessary to balance the load), and could it have been in the middle of a migration to another datastore when something occurred?
I had the same thing happen with ESXi 6.7 running on HP hardware and using the qfle3 module. Any chance you are running on HP?